/*
    Developer: John Archer (john.archer.jpa@gmail.com)
 
    This file is part of VTBuilder..

    VTBuilder is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License.

    VTBuilder is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with VTBuilder.  If not, see <http://www.gnu.org/licenses/>.
 */

package core.para;

import java.io.File;
public class Para {
    public static int MNRL =  150;
    public static int MNTLEN =  250;
    public static int TRDS = 12;
    public static String PATH_TO_FOWARD_READS = "";
    public static final String PATH_TO_REVERSE_READS_DEFAULT_VAL = "(optional)";
    public static String PATH_TO_REVERSE_READS = "";
    public static String PATH_TO_OUTPUT = "."+File.separator+"output.txt";
    public static String PATH_TO_LOGFILE = "."+File.separator+"log.txt";
    public static boolean GUI = true;
    public static int MEMORY_IN_GIGS = 30;
    public static String INITILIZER = "i";
    public static String LAUNCH_COMMAND = "";
    public static int MR = -1;
    public static int SD = -1;
    public static int NOS = -1;
    public static double KTDN = -1;
    public static int CLUST_SEQ_KT_TRANS = 96; 
    public static String SEPERATOR = "SSSSSSSSSSSSSSSSSSSS";
    public static String FILTERED_REV_FILE = "."+File.separator+"filteredRev";
    //this is the gui stuff that will be moved
    public static int START_VERTICAL_VIEW;
    public static int END_VERTICAL_VIEW;
    public static int START_HORIZONTAL_VIEW;
    public static int END_HORIZONTAL_VIEW;
    public static int X_AND_Y_APP_LOC = 100;
    public static String K_INIT = "-a";
    public static String K_FWREADS = "-b";
    public static String K_RVREADS = "-c";
    public static String K_OUTPUT = "-d";
    public static String K_LOG = "-e";
    public static String K_TRDS = "-f";
    public static String K_MRL = "-g";
    public static String K_MNTLEN = "-h";
    public static String K_SEARCHD = "-i";
    public static String K_TDIV = "-j";
}